1.11.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o固定一个缺陷在光大通信()可能会导致错误当执行同种型DE测试1样本与多个样本。1.9.3版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o GetDEResults帮助文件中正确的拼写错误。o包括规范化的一种备选方法。另一种方法是类似于median-by-ratio正常化,但可以处理的情况下,当所有的基因/亚型至少有一个零计数(在这种情况下,median-by-ratio正常化会失败)。这个替代方法是为单细胞RNA-seq开发分析数据集总是包含大量的零。1.9.2版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o固定一个错误时,可能会出现错误输入矩阵sizeFactors 1.9.1参数变化版本- - - - - - - - - - - - - - - - - - - - - - - - o在装饰图案来解决常见问题问答seqction变化版本1.7.1上- - - - - - - - - - - - - - - - - - - - - - - - o EBSeq 1.7.1上,EBSeq包含一个新的函数GetDEResults()可以用来获得一个列表记录下一个目标罗斯福在一个双态实验。结果通过应用这个函数的默认设置将更健壮的成绩单与低方差和潜在的离群值。通过使用默认设置在这个函数中,基因的数量确定在任何给定的分析可以从之前的版本略有不同(1.7.0或顺序)。获得的结果与早期版本的结果EBSeq(1.7.0以上),用户可以设置方法=“经典”GetDEResults()函数,或者使用原始GetPPMat()函数。GeneDEResults()函数还允许用户修改阈值与预先确定目标基因/亚型后褶皱的变化。 o Also, in EBSeq 1.7.1, the default settings in EBTest() and EBMultiTest() function will only remove transcripts with all 0's (instead of removing transcripts with 75th quantile less than 10 in version 1.3.3-1.7.0). To obtain a list of transcripts comparable to the results generated by EBSeq version 1.3.3-1.7.0, a user may change Qtrm = 0.75 and QtrmCut = 10 when applying EBTest() or EBMultiTest() function. CHANGES IN VERSION 1.5.4 ------------------------ o An extra numerical approximation step is implemented in EBMultiTest() function to avoid underflow. The underflow is likely due to large number of samples. A bug in EBMultiTest() is fixed. The bug will cause error when there is exactly 1 gene/isoform that needs numerical approximation. CHANGES IN VERSION 1.5.3 ------------------------- BUG FIXES o Fixed a bug that may generate NA FC estimates when there are no replicates. CHANGES IN VERSION 1.5.2 ------------------------ NEW FEATURES o An extra numerical approximation step is implemented in EBTest() function to avoid underflow. The underflow is likely due to large number of samples. CHANGES IN VERSION 1.3.3 ------------------------ NEW FEATURES o In EBSeq 1.3.3, the default setting of EBTest function will remove low expressed genes (genes whose 75th quantile of normalized counts is less than 10) before identifying DE genes. These two thresholds can be changed in EBTest function. Because low expressed genes are disproportionately noisy, removing these genes prior to downstream analyses can improve model fitting and increase robustness (e.g. by removing outliers).